durationEra is incorrect when eras are collapsed

[katy-sadowski]

Describe the bug
I have the following output in the patient level treatment hx table. durationEra is 29 but it should be longer. I checked the raw cohort data and this is a collapsed era of 2 overlapping events.

eventStartDate|eventEndDate|durationEra
2022-11-07 | 2023-01-06|29

To Reproduce
Run computePathways and specify an eraCollapseSize. Then inspect the output for a patient with collapsed eras.

Expected behavior
durationEra should represent the difference between era start and end for collapsed eras.

I think code needs to be added to doEraCollapse to recompute the duration:

[mvankessel-EMC]

Hi @katy-sadowski, I think this might already be resolved in the development branch, could you try that version:

remotes::install_github("darwin-eu-dev/TreatmentPatterns@develop")

[katy-sadowski]

I'm getting another bug in the develop branch. It doesn't seem to be adding the schema to my cohort table name:

Error in db_query_fields.DBIConnection():
! Can't query fields.
ℹ Using SQL: SELECT * FROM "cohort_202510_ra" "q01" WHERE (0 = 1)
Caused by error in value[[3L]]():
! net.snowflake.client.jdbc.SnowflakeSQLException: SQL compilation error:
Object '"cohort_202510_ra"' does not exist or not authorized.

[mvankessel-EMC]

Hi @katy-sadowski I missed this in the latest release of TreatmentPatterns. It should now be fixed in darwin-eu-dev/TreatmentPatterns. An alternative in the meantime is switching to a JDBC connection in the meantime.

You can do that either by 1) simply creating the regular ConnectionDetails from DatabaseConnector, and passing the relevant schemas to computePathways, or 2) create a cdm_reference using a a JDBC connection from DatabaseConnector

[katy-sadowski]

Thanks @mvankessel-EMC! However I was already passing a regular JDBC ConnectionDetails to computePathways when I got that error.